Bio::SeqIO MultiFile
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Summary
Bio::SeqIO::MultiFile - Treating a set of files as a single input stream
Package variables
No package variables defined.
Inherit
Bio::SeqIO
Synopsis
   $seqin = Bio::SeqIO::MultiFile( '-format' => 'Fasta',
'-files' => ['file1','file2'] );
while((my $seq = $seqin->next_seq)) {
# do something with $seq
}
Description
Bio::SeqIO::MultiFile provides a simple way of bundling a whole
set of identically formatted sequence input files as a single stream.
Methods
_initialize
No description
Code
next_seqDescriptionCode
next_primary_seqDescriptionCode
_load_fileDescriptionCode
_set_fileDescriptionCode
_current_seqioDescriptionCode
_formatDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage :
Function:
Example :
Returns :
Args :
next_primary_seqcodeprevnextTop
 Title   : next_primary_seq
Usage :
Function:
Example :
Returns :
Args :
_load_filecodeprevnextTop
 Title   : _load_file
Usage :
Function:
Example :
Returns :
Args :
_set_filecodeprevnextTop
 Title   : _set_file
Usage :
Function:
Example :
Returns :
Args :
_current_seqiocodeprevnextTop
 Title   : _current_seqio
Usage : $obj->_current_seqio($newval)
Function:
Example :
Returns : value of _current_seqio
Args : newvalue (optional)
_formatcodeprevnextTop
 Title   : _format
Usage : $obj->_format($newval)
Function:
Example :
Returns : value of _format
Args : newvalue (optional)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;

  $self->SUPER::_initialize(@args);

  my ($file_array,$format) = $self->_rearrange([qw(
					 FILES
					 FORMAT
					)],
				     @args,
				     );
  if( !defined $file_array || ! ref $file_array ) {
      $self->throw("Must have an array files for MultiFile");
  }

  if( !defined $format ) {
      $self->throw("Must have a format for MultiFile");
  }

  $self->{'_file_array'} = [];

  $self->_set_file(@$file_array);
  $self->_format($format);
  if( $self->_load_file() == 0 ) {
     $self->throw("Unable even to initialise the first file");
  }
}
next_seqdescriptionprevnextTop
sub next_seq {
   my ($self,@args) = @_;

   my $seq = $self->_current_seqio->next_seq();
   if( !defined $seq ) {
       if( $self->_load_file() == 0) {
	   return;
       } else {
	   return $self->next_seq();
       }
   } else {
       return $seq;
   }
}
next_primary_seqdescriptionprevnextTop
sub next_primary_seq {
   my ($self,@args) = @_;

   my $seq = $self->_current_seqio->next_primary_seq();
   if( !defined $seq ) {
       if( $self->_load_file() == 0) {
	   return;
       } else {
	   return $self->next_primary_seq();
       }
   } else {
       return $seq;
   }
}
_load_filedescriptionprevnextTop
sub _load_file {
   my ($self,@args) = @_;

   my $file = shift(@{$self->{'_file_array'}});
   if( !defined $file ) {
       return 0;
   }
   my $seqio = Bio::SeqIO->new( '-format' => $self->_format(), -file => $file);
   # should throw an exception - but if not...
if( !defined $seqio) { $self->throw("no seqio built for $file!"); } $self->_current_seqio($seqio); return 1;
}
_set_filedescriptionprevnextTop
sub _set_file {
   my ($self,@files) = @_;

   push(@{$self->{'_file_array'}},@files);
}
_current_seqiodescriptionprevnextTop
sub _current_seqio {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_current_seqio'} = $value;
    }
    return $obj->{'_current_seqio'};
}
_formatdescriptionprevnextTop
sub _format {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_format'} = $value;
    }
    return $obj->{'_format'};

}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _